1
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de Andrade KC, Strande NT, Kim J, Haley JS, Hatton JN, Frone MN, Khincha PP, Thone GM, Mirshahi UL, Schneider C, Desai H, Dove JT, Smelser DT, Levine AJ, Maxwell KN, Stewart DR, Carey DJ, Savage SA. Genome-first approach of the prevalence and cancer phenotypes of pathogenic or likely pathogenic germline TP53 variants. HGG ADVANCES 2024; 5:100242. [PMID: 37777824 PMCID: PMC10589747 DOI: 10.1016/j.xhgg.2023.100242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 09/20/2023] [Accepted: 09/20/2023] [Indexed: 10/02/2023] Open
Abstract
Pathogenic or likely pathogenic (P/LP) germline TP53 variants are the primary cause of Li-Fraumeni syndrome (LFS), a hereditary cancer predisposition disorder characterized by early-onset cancers. The population prevalence of P/LP germline TP53 variants is estimated to be approximately one in every 3,500 to 20,000 individuals. However, these estimates are likely impacted by ascertainment biases and lack of clinical and genetic data to account for potential confounding factors, such as clonal hematopoiesis. Genome-first approaches of cohorts linked to phenotype data can further refine these estimates by identifying individuals with variants of interest and then assessing their phenotypes. This study evaluated P/LP germline (variant allele fraction ≥30%) TP53 variants in three cohorts: UK Biobank (UKB, n = 200,590), Geisinger (n = 170,503), and Penn Medicine Biobank (PMBB, n = 43,731). A total of 109 individuals were identified with P/LP germline TP53 variants across the three databases. The TP53 p.R181H variant was the most frequently identified (9 of 109 individuals, 8%). A total of 110 cancers, including 47 hematologic cancers (47 of 110, 43%), were reported in 71 individuals. The prevalence of P/LP germline TP53 variants was conservatively estimated as 1:10,439 in UKB, 1:3,790 in Geisinger, and 1:2,983 in PMBB. These estimates were calculated after excluding related individuals and accounting for the potential impact of clonal hematopoiesis by excluding heterozygotes who ever developed a hematologic cancer. These varying estimates likely reflect intrinsic selection biases of each database, such as healthcare or population-based contexts. Prospective studies of diverse, young cohorts are required to better understand the population prevalence of germline TP53 variants and their associated cancer penetrance.
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Affiliation(s)
- Kelvin C de Andrade
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
| | - Natasha T Strande
- Department of Genomic Health, Geisinger Clinic, Geisinger, Danville, PA, USA
| | - Jung Kim
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jeremy S Haley
- Department of Genomic Health, Geisinger Clinic, Geisinger, Danville, PA, USA
| | - Jessica N Hatton
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Megan N Frone
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Payal P Khincha
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Gretchen M Thone
- Department of Genomic Health, Geisinger Clinic, Geisinger, Danville, PA, USA
| | - Uyenlinh L Mirshahi
- Department of Genomic Health, Geisinger Clinic, Geisinger, Danville, PA, USA
| | - Cynthia Schneider
- Division of Hematology/Oncology, Department of Medicine and Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Heena Desai
- Division of Hematology/Oncology, Department of Medicine and Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - James T Dove
- Department of Genomic Health, Geisinger Clinic, Geisinger, Danville, PA, USA
| | - Diane T Smelser
- Department of Genomic Health, Geisinger Clinic, Geisinger, Danville, PA, USA
| | - Arnold J Levine
- Simons Center for Systems Biology, Institute for Advanced Study, Princeton, NJ, USA
| | - Kara N Maxwell
- Division of Hematology/Oncology, Department of Medicine and Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Douglas R Stewart
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - David J Carey
- Department of Genomic Health, Geisinger Clinic, Geisinger, Danville, PA, USA
| | - Sharon A Savage
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
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2
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Truty R, Rojahn S, Ouyang K, Kautzer C, Kennemer M, Pineda-Alvarez D, Johnson B, Stafford A, Basel-Salmon L, Saitta S, Slavotinek A, Chandrasekharappa SC, Suarez CJ, Burnett L, Nussbaum RL, Aradhya S. Patterns of mosaicism for sequence and copy-number variants discovered through clinical deep sequencing of disease-related genes in one million individuals. Am J Hum Genet 2023; 110:551-564. [PMID: 36933558 PMCID: PMC10119133 DOI: 10.1016/j.ajhg.2023.02.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 02/23/2023] [Indexed: 03/19/2023] Open
Abstract
DNA variants that arise after conception can show mosaicism, varying in presence and extent among tissues. Mosaic variants have been reported in Mendelian diseases, but further investigation is necessary to broadly understand their incidence, transmission, and clinical impact. A mosaic pathogenic variant in a disease-related gene may cause an atypical phenotype in terms of severity, clinical features, or timing of disease onset. Using high-depth sequencing, we studied results from one million unrelated individuals referred for genetic testing for almost 1,900 disease-related genes. We observed 5,939 mosaic sequence or intragenic copy number variants distributed across 509 genes in nearly 5,700 individuals, constituting approximately 2% of molecular diagnoses in the cohort. Cancer-related genes had the most mosaic variants and showed age-specific enrichment, in part reflecting clonal hematopoiesis in older individuals. We also observed many mosaic variants in genes related to early-onset conditions. Additional mosaic variants were observed in genes analyzed for reproductive carrier screening or associated with dominant disorders with low penetrance, posing challenges for interpreting their clinical significance. When we controlled for the potential involvement of clonal hematopoiesis, most mosaic variants were enriched in younger individuals and were present at higher levels than in older individuals. Furthermore, individuals with mosaicism showed later disease onset or milder phenotypes than individuals with non-mosaic variants in the same genes. Collectively, the large compendium of variants, disease correlations, and age-specific results identified in this study expand our understanding of the implications of mosaic DNA variation for diagnosis and genetic counseling.
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Affiliation(s)
- Rebecca Truty
- Invitae, 1400 16th Street, San Francisco, CA 94103, USA
| | - Susan Rojahn
- Invitae, 1400 16th Street, San Francisco, CA 94103, USA
| | - Karen Ouyang
- Invitae, 1400 16th Street, San Francisco, CA 94103, USA
| | | | | | | | - Britt Johnson
- Invitae, 1400 16th Street, San Francisco, CA 94103, USA
| | | | - Lina Basel-Salmon
- Rabin Medical Center-Beilinson Hospital and Schneider Children's Medical Center of Israel, Petach Tikva, Israel; Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel; Felsenstein Medical Research Center, Petach Tikva, Israel
| | - Sulagna Saitta
- Division of Clinical Genetics, Departments of Pediatrics and Obstetrics and Gynecology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Anne Slavotinek
- Division of Human Genetics, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Settara C Chandrasekharappa
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Carlos Jose Suarez
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94301, USA
| | | | - Robert L Nussbaum
- Invitae, 1400 16th Street, San Francisco, CA 94103, USA; School of Medicine, University of California - San Francisco, San Francisco, CA, USA
| | - Swaroop Aradhya
- Invitae, 1400 16th Street, San Francisco, CA 94103, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA 94301, USA.
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3
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Chen JL, Miller DT, Schmidt LS, Malkin D, Korf BR, Eng C, Kwiatkowski DJ, Giannikou K. Mosaicism in Tumor Suppressor Gene Syndromes: Prevalence, Diagnostic Strategies, and Transmission Risk. Annu Rev Genomics Hum Genet 2022; 23:331-361. [PMID: 36044908 DOI: 10.1146/annurev-genom-120121-105450] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
A mosaic state arises when pathogenic variants are acquired in certain cell lineages during postzygotic development, and mosaic individuals may present with a generalized or localized phenotype. Here, we review the current state of knowledge regarding mosaicism for eight common tumor suppressor genes-NF1, NF2, TSC1, TSC2, PTEN, VHL, RB1, and TP53-and their related genetic syndromes/entities. We compare and discuss approaches for comprehensive diagnostic genetic testing, the spectrum of variant allele frequency, and disease severity. We also review affected individuals who have no mutation identified after conventional genetic analysis, as well as genotype-phenotype correlations and transmission risk for each tumor suppressor gene in full heterozygous and mosaic patients. This review provides new insight into similarities as well as marked differences regarding the appreciation of mosaicism in these tumor suppressor syndromes.
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Affiliation(s)
- Jillian L Chen
- Cancer Genetics Laboratory, Division of Pulmonary and Critical Care Medicine and Division of Genetics, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA; .,Boston University School of Medicine, Boston, Massachusetts, USA
| | - David T Miller
- Division of Genetics and Genomics, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Laura S Schmidt
- Urologic Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA.,Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - David Malkin
- Division of Haematology/Oncology, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Pediatrics, University of Toronto, Toronto, Ontario, Canada
| | - Bruce R Korf
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Charis Eng
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA.,Taussig Cancer Institute, Cleveland Clinic, Cleveland, Ohio, USA.,Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA.,Germline High Risk Cancer Focus Group, Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, Ohio, USA
| | - David J Kwiatkowski
- Cancer Genetics Laboratory, Division of Pulmonary and Critical Care Medicine and Division of Genetics, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA;
| | - Krinio Giannikou
- Cancer Genetics Laboratory, Division of Pulmonary and Critical Care Medicine and Division of Genetics, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA; .,Division of Hematology and Oncology, Cancer and Blood Disease Institute, Children's Hospital Los Angeles, Los Angeles, California, USA;
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4
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Castillo D, Yuan TA, Nehoray B, Cervantes A, Tsang KK, Yang K, Sand SR, Mokhnatkin J, Herzog J, Slavin TP, Hyman S, Schwartz A, Ebert BL, Amos CI, Garber JE, Weitzel JN. Clonal Hematopoiesis and Mosaicism Revealed by a Multi-Tissue Analysis of Constitutional TP53 Status. Cancer Epidemiol Biomarkers Prev 2022; 31:1621-1629. [PMID: 35654360 PMCID: PMC9866580 DOI: 10.1158/1055-9965.epi-21-1296] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 02/02/2022] [Accepted: 05/20/2022] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Though germline TP53 pathogenic/likely pathogenic variants (PV) are associated with Li-Fraumeni syndrome, many detected by multigene panels represent aberrant clonal expansion (ACE), most due to clonal hematopoiesis (CH). Discerning ACE/CH from germline variants and postzygotic mosaicism (PZM) is critically needed for risk assessment and management. METHODS Participants in the Li-Fraumeni & TP53 Understanding & Progress (LiFT UP) study with a TP53 PV were eligible. Demographics, personal/family cancer history, and clinical laboratory test reports were obtained. DNA from multiple tissues was analyzed using a custom QIAseq assay (ACE panel) that included TP53 and other CH-associated genes; the ACE panel and eyebrow follicles were assessed in a workflow to discern TP53 PV clinical categories. RESULTS Among 134 participants there was a significant difference for the age at diagnosis (P < 0.001), component cancers (P = 0.007), and clinical testing criteria (P < 0.001), comparing germline with PZM or ACE. ACE panel analysis of DNA from 55 sets of eyebrow follicles (mean 1.4 ug) and 36 formalin-fixed, paraffin imbedded tissues demonstrated low variance (SE, 3%; P = 0.993) for TP53 variant allele fraction, with no significant difference (P = 0.965) between tissue types, and detected CH gene PVs. Of 55 multi-tissue cases, germline status was confirmed for 20, PZM in seven, ACE for 25, and three were indeterminate. Additional CH variants were detected in six ACE and two germline cases. CONCLUSIONS We demonstrated an effective approach and tools for discerning germline TP53 status. IMPACT Discernment of PZM and TP53-driven CH increases diagnostic accuracy and enables risk-appropriate care.
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Affiliation(s)
| | - Tze-An Yuan
- City of Hope Cancer Center, Duarte, CA 91010, USA
| | - Bita Nehoray
- City of Hope Cancer Center, Duarte, CA 91010, USA
| | | | | | - Kai Yang
- City of Hope Cancer Center, Duarte, CA 91010, USA
| | | | | | - Josef Herzog
- City of Hope Cancer Center, Duarte, CA 91010, USA
| | | | - Sophie Hyman
- Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | | | | | | | | | - Jeffrey N. Weitzel
- City of Hope Cancer Center, Duarte, CA 91010, USA
- Latin American School of Oncology, Los Angeles, CA, USA
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5
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Sutcliffe EG, Mester JL, Susswein LR, Roberts ME, Marshall ML, Hruska KS. Fibroblast testing can inform medical management in individuals with mosaic variants detected on hereditary cancer panels. Cancer Genet 2022; 266-267:86-89. [DOI: 10.1016/j.cancergen.2022.07.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 06/08/2022] [Accepted: 07/23/2022] [Indexed: 11/30/2022]
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6
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Steensma DP. How predictive is the finding of clonal hematopoiesis for the development of myelodysplastic syndromes (MDS) or acute myeloid leukemia (AML)? Best Pract Res Clin Haematol 2021; 34:101327. [PMID: 34865699 DOI: 10.1016/j.beha.2021.101327] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Clonal hematopoiesis (CH) - a biological state in which one or a small number of hematopoietic stem or progenitor cells contribute disproportionately to blood cell production, usually as a result of somatic gene mutations in the stem cells - is often considered to be a precursor to myeloid neoplasia, especially myelodysplastic syndromes (MDS) and acute myeloid leukemia (AML). However, the majority of people with CH never develop an overt myeloid neoplasm, and CH can be a precursor to lymphoid cancers as well as myeloid neoplasms. In addition, CH increases all-cause mortality and augments the risk of several non-neoplastic medical conditions, including atherosclerotic cardiovascular disease. CH can arise during aging, or in the context of an inherited marrow failure syndrome, aplastic anemia, or hematopoietic cell transplantation. Risk factors for progression of CH to myeloid neoplasia include larger clone size; the presence of a TP53, IDH1/2, or splicing mutation; multiple mutations; and associated cytopenias or abnormal red blood cell indices. The receipt of genotoxic chemotherapy or radiation, which can promote clonal expansion of mutant clones at the expense of healthy progenitor cells, may result in therapy-related MDS/AML.
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7
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Fortuno C, McGoldrick K, Pesaran T, Dolinsky J, Hoang L, Weitzel JN, Beshay V, San Leong H, James PA, Spurdle AB. Suspected clonal hematopoiesis as a natural functional assay of TP53 germline variant pathogenicity. Genet Med 2021; 24:673-680. [PMID: 34906512 DOI: 10.1016/j.gim.2021.10.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 10/22/2021] [Accepted: 10/25/2021] [Indexed: 10/19/2022] Open
Abstract
PURPOSE Some variants identified by multigene panel testing of DNA from blood present with low variant allele fraction (VAF), often a manifestation of clonal hematopoiesis. Research has shown that the proportion of variants with low VAF is especially high in TP53, the Li-Fraumeni syndrome gene. Based on the hypothesis that variants with low VAF are positively selected as drivers of clonal hematopoiesis, we investigated the use of VAF as a predictor of TP53 germline variant pathogenicity. METHODS We used data from 260,681 TP53 variants identified at 2 laboratories to compare the distribution of pathogenic and benign variants at different VAF intervals. RESULTS Likelihood ratios toward pathogenicity associated with a VAF < 26% equated to the American College of Medical Genetics/Association of Molecular Pathology strong strength level and were applicable for 1 in 5 variants of unknown significance. CONCLUSION In conclusion, detection of variants with low VAF in blood can be considered an in vivo functional assay to aid assessment of TP53 variant pathogenicity.
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Affiliation(s)
- Cristina Fortuno
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | | | | | | | | | | | - Victoria Beshay
- Molecular Pathology Laboratory, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Huei San Leong
- Molecular Pathology Laboratory, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Paul A James
- Parkville Familial Cancer Centre, Peter MacCallum Cancer Centre, and Royal Melbourne Hospital, Melbourne, Victoria, Australia; Sir Peter MacCallum Department of Oncology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Victoria, Australia.
| | - Amanda B Spurdle
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia.
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8
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Schwartz AN, Hyman SR, Stokes SM, Castillo D, Tung NM, Weitzel JN, Rana HQ, Garber JE. Evaluation of TP53 Variants Detected on Peripheral Blood or Saliva Testing: Discerning Germline From Somatic TP53 Variants. JCO Precis Oncol 2021; 5:1677-1686. [PMID: 34994652 DOI: 10.1200/po.21.00278] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 09/15/2021] [Accepted: 09/24/2021] [Indexed: 01/04/2023] Open
Abstract
PURPOSE Multigene panel testing (MGPT) identifies TP53 pathogenic or likely pathogenic (P/LP) variants in patients with diverse phenotypes, of which only one is classic Li-Fraumeni syndrome. Low variant allelic fraction (VAF) in TP53 found on germline testing may suggest aberrant clonal expansion or constitutional mosaicism. We evaluated TP53-positive probands seen in a cancer genetics program to determine germline versus somatic status. METHODS We reviewed TP53-positive probands from 2012 to 2019 identified by MGPT on blood or saliva (N = 84). Available VAFs were collected. Probands with a familial variant, who met Li-Fraumeni syndrome testing criteria or who carried a founder variant, were considered germline. For those with uncertain germline status, TP53 variants were further examined using ancillary data of family members and somatic tissue. RESULTS Of the 84 probands, 54.7% had germline variants with 33.3% meeting criteria for germline status and 21.4% confirmed through ancillary testing. Aberrant clonal expansion comprised 13.1% with clonal hematopoiesis of indeterminate potential and 2.4% with a hematologic malignancy. Constitutional mosaicism was confirmed in 8.3% probands. Definitive status could not be determined in 3.6% despite ancillary assessment, and 17.9% did not have ancillary testing. CONCLUSION A TP53 P/LP variant found on peripheral blood or saliva MGPT does not always originate in the germline. In a clinical cancer genetics cohort, approximately half of the patients had TP53 P/LP germline variants; these patients plus those with constitutional mosaicism require intensified surveillance. A framework of multiple strategies enables discernment of germline from constitutional mosaic and acquired variants, which is essential for appropriate management.
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Affiliation(s)
- Alison N Schwartz
- Division of Cancer Genetics and Prevention, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Sophie R Hyman
- Division of Cancer Genetics and Prevention, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Samantha M Stokes
- Division of Cancer Genetics and Prevention, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Danielle Castillo
- Division of Clinical Cancer Genomics, Beckman Research Institute, City of Hope, Duarte, CA
| | - Nadine M Tung
- Harvard Medical School, Boston, MA
- Division of Hematology and Oncology, Beth Israel Deaconess Medical Center, Boston, MA
| | | | - Huma Q Rana
- Division of Cancer Genetics and Prevention, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Harvard Medical School, Boston, MA
| | - Judy E Garber
- Division of Cancer Genetics and Prevention, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Harvard Medical School, Boston, MA
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9
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Maani N, Panabaker K, McCuaig JM, Buckley K, Semotiuk K, Farncombe KM, Ainsworth P, Panchal S, Sadikovic B, Armel SR, Lin H, Kim RH. Incidental findings from cancer next generation sequencing panels. NPJ Genom Med 2021; 6:63. [PMID: 34282142 PMCID: PMC8289933 DOI: 10.1038/s41525-021-00224-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Accepted: 06/09/2021] [Indexed: 11/09/2022] Open
Abstract
Next-generation sequencing (NGS) technologies have facilitated multi-gene panel (MGP) testing to detect germline DNA variants in hereditary cancer patients. This sensitive technique can uncover unexpected, non-germline incidental findings indicative of mosaicism, clonal hematopoiesis (CH), or hematologic malignancies. A retrospective chart review was conducted to identify cases of incidental findings from NGS-MGP testing. Inclusion criteria included: 1) multiple pathogenic variants in the same patient; 2) pathogenic variants at a low allele fraction; and/or 3) the presence of pathogenic variants not consistent with family history. Secondary tissue analysis, complete blood count (CBC) and medical record review were conducted to further delineate the etiology of the pathogenic variants. Of 6060 NGS-MGP tests, 24 cases fulfilling our inclusion criteria were identified. Pathogenic variants were detected in TP53, ATM, CHEK2, BRCA1 and APC. 18/24 (75.0%) patients were classified as CH, 3/24 (12.5%) as mosaic, 2/24 (8.3%) related to a hematologic malignancy, and 1/24 (4.2%) as true germline. We describe a case-specific workflow to identify and interpret the nature of incidental findings on NGS-MGP. This workflow will provide oncology and genetic clinics a practical guide for the management and counselling of patients with unexpected NGS-MGP findings.
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Affiliation(s)
- Nika Maani
- Program for Genetics and Genome Biology, Hospital for Sick Children, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Karen Panabaker
- Medical Genetics Program of Southwestern Ontario, London Health Sciences Centre, London, ON, Canada
| | - Jeanna M McCuaig
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.,Familial Cancer Clinic, Princess Margaret Hospital Cancer Centre, Toronto, ON, Canada
| | | | - Kara Semotiuk
- Zane Cohen Centre for Digestive Diseases, Familial Gastrointestinal Cancer Registry, Mount Sinai Hospital, Toronto, ON, Canada
| | - Kirsten M Farncombe
- Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada
| | - Peter Ainsworth
- Molecular Genetics Laboratory, Division of Molecular Diagnostics, London Health Sciences Centre, London, ON, Canada
| | - Seema Panchal
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.,Familial Breast Cancer Clinic, Mount Sinai Hospital, Toronto, ON, Canada
| | - Bekim Sadikovic
- Molecular Genetics Laboratory, Division of Molecular Diagnostics, London Health Sciences Centre, London, ON, Canada.,Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Susan Randall Armel
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.,Familial Cancer Clinic, Princess Margaret Hospital Cancer Centre, Toronto, ON, Canada
| | - Hanxin Lin
- Molecular Genetics Laboratory, Division of Molecular Diagnostics, London Health Sciences Centre, London, ON, Canada. .,Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada.
| | - Raymond H Kim
- Familial Cancer Clinic, Princess Margaret Hospital Cancer Centre, Toronto, ON, Canada. .,Department of Medicine, University of Toronto, Toronto, ON, Canada.
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10
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Fortuno C, Pesaran T, Dolinsky J, Yussuf A, McGoldrick K, Tavtigian SV, Goldgar D, Spurdle AB, James PA. An updated quantitative model to classify missense variants in the TP53 gene: A novel multifactorial strategy. Hum Mutat 2021; 42:1351-1361. [PMID: 34273903 DOI: 10.1002/humu.24264] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 06/25/2021] [Accepted: 07/15/2021] [Indexed: 11/07/2022]
Abstract
Multigene panel testing has led to an increase in the number of variants of uncertain significance identified in the TP53 gene, associated with Li-Fraumeni syndrome. We previously developed a quantitative model for predicting the pathogenicity of P53 missense variants based on the combination of calibrated bioinformatic information and somatic to germline ratio. Here, we extended this quantitative model for the classification of P53 predicted missense variants by adding new pieces of evidence (personal and family history parameters, loss-of-function results, population allele frequency, healthy individual status by age 60, and breast tumor pathology). We also annotated which missense variants might have an effect on splicing based on bioinformatic predictions. This updated model plus annotation led to the classification of 805 variants into a clinically relevant class, which correlated well with existing ClinVar classifications, and resolved a large number of conflicting and uncertain classifications. We propose this model as a reliable approach to TP53 germline variant classification and emphasize its use in contributing to optimize TP53-specific ACMG/AMP guidelines.
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Affiliation(s)
- Cristina Fortuno
- Genetics and Computational Division, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | | | | | - Amal Yussuf
- Ambry Genetics, Aliso Viejo, California, USA
| | | | - Sean V Tavtigian
- Huntsman Cancer Institute and Department of Dermatology, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - David Goldgar
- Huntsman Cancer Institute and Department of Dermatology, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Amanda B Spurdle
- Genetics and Computational Division, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Paul A James
- Parkville Familial Cancer Centre, Peter MacCallum Cancer Centre and Royal Melbourne Hospital, Melbourne, Australia
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11
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DiNardo CD, Korde LA, Yurgelun MB. A Case-Based Approach to Understanding Complex Genetic Information in an Evolving Landscape. Am Soc Clin Oncol Educ Book 2021; 41:1-11. [PMID: 34010053 DOI: 10.1200/edbk_321041] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The rapid integration of highly sensitive next-generation sequencing technologies into clinical oncology care has led to unparalleled progress, and yet these technological advances have also made genetic information considerably more complex. For instance, accurate interpretation of genetic testing for germline/inherited cancer predisposition syndromes and somatic/acquired pathogenic variants now requires a more nuanced understanding of the presence and incidence of clonal hematopoiesis and circulating tumor cells, with careful evaluation of pathogenic variants occurring at low variant allele frequency required. The interplay between somatic and germline pathogenic variants and awareness of distinct genotype-phenotype manifestations in various inherited cancer syndromes are now increasingly appreciated and can impact patient management. Through a case-based approach, we focus on three areas of particular relevance to the treating clinician oncologist: (1) understanding clonal hematopoiesis and somatic mosaicism, which can be detected on germline sequencing and lead to considerable confusion in clinical interpretation; (2) implications of the detection of a potentially germline pathogenic variant in a high-penetrance cancer susceptibility gene during routine tumor testing; and (3) a review of gene-specific risks and surveillance recommendations in Lynch syndrome. A discussion on the availability and difficulties often associated with direct-to-consumer genetic testing is also provided.
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Affiliation(s)
- Courtney D DiNardo
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Matthew B Yurgelun
- Dana-Farber Cancer Institute, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA
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Evans DG, Woodward ER. New surveillance guidelines for Li-Fraumeni and hereditary TP53 related cancer syndrome: implications for germline TP53 testing in breast cancer. Fam Cancer 2020; 20:1-7. [PMID: 32984917 DOI: 10.1007/s10689-020-00207-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- D Gareth Evans
- Division of Evolution and Genomic Sciences, Manchester Centre for Genomic Medicine, University of Manchester, Manchester Academic Health Sciences Centre (MAHSC), St Mary's Hospital, Manchester University Hospitals NHS Foundation Trust, Manchester, UK.
| | - Emma R Woodward
- Division of Evolution and Genomic Sciences, Manchester Centre for Genomic Medicine, University of Manchester, Manchester Academic Health Sciences Centre (MAHSC), St Mary's Hospital, Manchester University Hospitals NHS Foundation Trust, Manchester, UK
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Fortuno C, Pesaran T, Mester J, Dolinsky J, Yussuf A, McGoldrick K, James PA, Spurdle AB. Genotype-phenotype correlations among TP53 carriers: Literature review and analysis of probands undergoing multi-gene panel testing and single-gene testing. Cancer Genet 2020; 248-249:11-17. [PMID: 32966936 DOI: 10.1016/j.cancergen.2020.09.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 08/18/2020] [Accepted: 09/08/2020] [Indexed: 01/16/2023]
Abstract
Pathogenic germline variants in the TP53 gene predispose to a wide range of cancers, known collectively as Li-Fraumeni syndrome (LFS). There has been much research aimed to identify genotype-phenotype correlations, that is, differences between variant location and/or effect and cancer spectrum. These correlations, should they exist, have potential to impact clinical management of carriers. Review of previously published studies showed a variety of study designs and inconsistency in reported findings. Here, we used pooled data from 427 TP53 carriers who had undergone multigene panel testing and 154 TP53 carriers identified by single-gene testing to investigate correlations between TP53 genotype (truncating variants, hotspot variants, other missense variants with dominant-negative effect, missense variants without dominant-negative effect) and a number of LFS-selected malignancies. Our results suggest that carriers of truncating and hotspot variants might be more likely to present with LFS cancers and have shorter time to first cancer diagnosis compared to carriers of other variant types. However, the differences observed were minor, and we conclude that there is currently insufficient evidence to consider location and/or molecular effect of pathogenic variants to assist with clinical management of TP53 carriers. Larger studies are necessary to confirm the correlations suggested by our analysis.
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Affiliation(s)
- Cristina Fortuno
- QIMR Berghofer Medical Research Institute, Genetics and Computational Division, 300 Herston Rd, Herston, QLD 4006, Australia
| | | | | | | | | | | | - Paul A James
- Parkville Familial Cancer Centre, Peter MacCallum Cancer Centre and Royal Melbourne Hospital, Australia
| | - Amanda B Spurdle
- QIMR Berghofer Medical Research Institute, Genetics and Computational Division, 300 Herston Rd, Herston, QLD 4006, Australia.
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Pre- and Post-Zygotic TP53 De Novo Mutations in SHH-Medulloblastoma. Cancers (Basel) 2020; 12:cancers12092503. [PMID: 32899294 PMCID: PMC7564492 DOI: 10.3390/cancers12092503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 08/26/2020] [Accepted: 09/01/2020] [Indexed: 11/26/2022] Open
Abstract
Simple Summary Medulloblastoma is the most common malignant brain tumor in children. In a subset of cases, a causal factor is a constitutive mutation of the TP53 gene, which may be inherited or arise for the first time in a patient (de novo). Using an immunohistochemistry assay as a screening tool, we selected patients suspected of harboring a TP53 mutation and offered genetic counseling and germline testing. Our study, which was the first to investigate the parental origin of TP53 mutations in medulloblastoma, allowed the identification of two additional cases with de novo mutations. Moreover, we demonstrated that in one patient the mutation originated at a post-zygotic stage, resulting in somatic mosaicism. These findings have important implications for genetic counseling since they highlight the occurrence of both pre- and post-zygotic TP53 de novo mutations in medulloblastoma, pointing out that in a specific subgroup of patients genetic testing should be offered regardless of family history. Abstract Li-Fraumeni syndrome (LFS) is an autosomal dominant disorder caused by mutations in the TP53 gene, predisposing to a wide spectrum of early-onset cancers, including brain tumors. In medulloblastoma patients, the role of TP53 has been extensively investigated, though the prevalence of de novo mutations has not been addressed. We characterized TP53 mutations in a monocentric cohort of consecutive Sonic Hedgehog (SHH)-activated medulloblastoma patients. Germline testing was offered based on tumor p53 immunostaining positivity. Among 24 patients, three (12.5%) showed tumor p53 overexpression, of whom two consented to undergo germline testing and resulted as carriers of TP53 mutations. In the first case, family history was uneventful and the mutation was not found in either of the parents. The second patient, with a family history suggestive of LFS, unexpectedly resulted as a carrier of the mosaic mutation c.742=/C>T p.(Arg248=/Trp). The allele frequency was 26% in normal tissues and 42–77% in tumor specimens. Loss of heterozygosity (LOH) in the tumor was also confirmed. Notably, the mosaic case has been in complete remission for more than one year, while the first patient, as most TP53-mutated medulloblastoma cases from other cohorts, showed a severe and rapidly progressive disease. Our study reported the first TP53 mosaic mutation in medulloblastoma patients and confirmed the importance of germline testing in p53 overexpressed SHH-medulloblastoma, regardless of family history.
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Fortuno C, Mester J, Pesaran T, Weitzel JN, Dolinsky J, Yussuf A, McGoldrick K, Garber JE, Savage SA, Khincha PP, Evans DG, Achatz MI, Nichols KE, Maxwell K, Schiffman JD, Sandoval R, James PA, Spurdle AB. Suggested application of HER2+ breast tumor phenotype for germline TP53 variant classification within ACMG/AMP guidelines. Hum Mutat 2020; 41:1555-1562. [PMID: 32485079 PMCID: PMC7484289 DOI: 10.1002/humu.24060] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 03/21/2020] [Accepted: 05/18/2020] [Indexed: 01/01/2023]
Abstract
Early onset breast cancer is the most common malignancy in women with Li-Fraumeni syndrome, caused by germline TP53 pathogenic variants. It has repeatedly been suggested that breast tumors from TP53 carriers are more likely to be HER2+ than those of noncarriers, but this information has not been incorporated into variant interpretation models for TP53. Breast tumor pathology is already being used quantitatively for assessing pathogenicity of germline variants in other genes, and it has been suggested that this type of evidence can be incorporated into current American College of Medical Genetics and Genomics/Association for Molecular Pathology (ACMG/AMP) guidelines for germline variant classification. Here, by reviewing published data and using internal datasets separated by different age groups, we investigated if breast tumor HER2+ status has utility as a predictor of TP53 germline variant pathogenicity, considering age at diagnosis. Overall, our results showed that the identification of HER2+ breast tumors diagnosed before the age of 40 can be conservatively incorporated into the current TP53-specific ACMG/AMP PP4 criterion, following a point system detailed in this manuscript. Further larger studies will be needed to reassess the value of HER2+ breast tumors diagnosed at a later age.
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Affiliation(s)
- Cristina Fortuno
- QIMR Berghofer Medical Research Institute, Genetics and Computational Division, 300 Herston Rd, Herston QLD 4006, Australia
| | | | | | - Jeffrey N. Weitzel
- Clinical Cancer Genomics, City of Hope Comprehensive Cancer Center, Duarte, CA
| | | | | | | | - Judy E. Garber
- Center for Cancer Genetics and Prevention, Dana Farber Cancer Institute, Boston, MA
| | - Sharon A. Savage
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Payal P. Khincha
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - D. Gareth Evans
- University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | | | | | | | | | | | - Paul A. James
- Parkville Familial Cancer Centre, Peter MacCallum Cancer Centre and Royal Melbourne Hospital
| | - Amanda B. Spurdle
- QIMR Berghofer Medical Research Institute, Genetics and Computational Division, 300 Herston Rd, Herston QLD 4006, Australia
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Coombs CC, Dickherber T, Crompton BD. Chasing ctDNA in Patients With Sarcoma. Am Soc Clin Oncol Educ Book 2020; 40:e351-e360. [PMID: 32598183 DOI: 10.1200/edbk_280749] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Liquid biopsies are new technologies that allow cancer profiling of tumor fragments found in body fluids, such as peripheral blood, collected noninvasively from patients with malignancies. These assays are increasingly valuable in clinical oncology practice as prognostic biomarkers, as guides for therapy selection, for treatment monitoring, and for early detection of disease progression and relapse. However, application of these assays to rare cancers, such as pediatric and adult sarcomas, have lagged. In this article, we review the technical challenges of applying liquid biopsy technologies to sarcomas, provide an update on progress in the field, describe common pitfalls in interpreting liquid biopsy data, and discuss the intersection of sarcoma clinical care and commercial assays emerging on the horizon.
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Affiliation(s)
| | | | - Brian D Crompton
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA
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Pederson HJ, Noss R. Updates in hereditary breast cancer genetic testing and practical high risk breast management in gene carriers. Semin Oncol 2020; 47:182-186. [PMID: 32513422 DOI: 10.1053/j.seminoncol.2020.05.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 05/04/2020] [Accepted: 05/04/2020] [Indexed: 11/11/2022]
Abstract
Testing for hereditary predisposition to breast cancer is rapidly expanding in parallel with the emerging field of molecular genetics given the associated implications for screening, risk reduction and cancer therapeutics for identified gene mutation carriers. With the advent of next generation multigene panel testing for hereditary predisposition and decreasing cost for that testing, more breast cancer patients (and unaffected family members) are undergoing cancer genetic testing. With multiple genes being tested and the myriad of possible results and implications for patients and their families, the process of genetic counseling is of paramount importance in promoting understanding by both patients and providers of risks and options for risk management. Guidelines exist to facilitate a multidisciplinary approach to management of individuals identified as being at increased risk, and there must be an appreciation for flexibility as guidelines are applied to individual families. This update summarizes recommendations regarding who may benefit from breast cancer risk assessment and genetic counseling, controversies regarding inclusion for testing and provides a framework for the practical management of high risk gene carriers.
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Affiliation(s)
- Holly J Pederson
- Cleveland Clinic, Breast Center - Departments of General Surgery and Genomic Medicine Institute, Cleveland, OH.
| | - Ryan Noss
- Cleveland Clinic, Breast Center - Departments of General Surgery and Genomic Medicine Institute, Cleveland, OH
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